There are substantial discrepancies in risk assessments of transgenic maize in Europe. The aim of the study was to determine the quantitative changes in the proportion of fungi-infected aphids and possible differences in the species composition of entomopathogenic fungi on conventional and genetically modified maize, expressing Cry1Ab protein from Bacillus thuringiensis (Bt). The experiments were performed in Lower Silesia, Poland, in 2008-2010. Three cultivars were used, i.e. DKC 3421 YG (Bt), isogenic non-Bt DKC 3420, and the conventional 'Bosman' as a reference. Aphids infected with fungi were counted in situ on 18 plants per plot every two weeks through each of the growing seasons. Additionally, twice a year dead aphids were also collected (60 aphids per treatment) and used for fungi identification. Cry1Ab insecticidal protein had no effect on the incidence of entomopathogenic fungi infecting aphids on Bt maize. The number of fungi-infected aphids and their time of occurrence were similar on the three compared cultivars. The same three or four species of entomopathogenic fungi-infected aphids were found in each treatment. Predominating in all the treatments were Pandora neoaphidis, Entomophthora planchoniana and Conidiobolus thromboides.